I used Aegean Thesaurus Travel (recommended by fellow forumer) when I visited Greece in Oct 06. They are good. Check out their website.
http://www.thesaurus.gr/index.htm
I booked their 4 day classic land tour which was professionally conducted. The hotels during those few nights were good. People on the same tour group (mostly Canadians, Americans, a couple of NZ) were fabulous and very punctual. Very good experience. Would suggest this rather than drive around as the tour guide will give you a very good insight into the history of the places you will visit. Else, you will just be seeing lots of ruins without understanding the history if you do it yourself.
Aegean Thesaurus also assisted in booking accomodation, ferry bookings, port transfers, airport transfers for us. I suggest booking hotels from them as they seem to be able to get better prices, even lower than those published in the hotel's website.
Book ferry tickets with them as well. They will call you if the ferry is cancelled so that you do not need to make a wasted trip to the port. I know because our ferry to Santorini was cancelled due to bad weather and Aegean called me in the morning to arrange for another night stay in Athens (it was a night ferry).
You can practically booked everything with them. They don't charge you extra, eg ferry prices charged were similar to prices printed on tickets. I think they get a commission cut from the hotels, ferry co etc. But they do charge a few tens of Euros for mailing our ferry tickets to our Athens hotel though.
As for safety concerns, Greece is a safe country. I felt safer in Greece than say Spain or France which are very safe also. Note: I travel F&E in France and Spain. Of course you do however need to take the usual precaution in taking care of your stuff like not leaving your handbag unattended, unzipped etc.